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annotate overlay_images.xml @ 5:002f7bad3e82 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:58 +0000
parents 37662cbf44b8
children 2495f8b2aefd
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37662cbf44b8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
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1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description></description>
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3 <macros>
5
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4 <import>creators.xml</import>
002f7bad3e82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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5 <import>tests.xml</import>
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6 <token name="@TOOL_VERSION@">0.0.4</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
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8 </macros>
5
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9 <creator>
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10 <expand macro="creators/bmcv"/>
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11 <expand macro="creators/thawn"/>
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12 </creator>
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13 <edam_operations>
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14 <edam_operation>operation_3443</edam_operation>
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15 </edam_operations>
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16 <xrefs>
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17 <xref type="bio.tools">galaxy_image_analysis</xref>
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18 </xrefs>
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19 <requirements>
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20 <requirement type="package" version="0.18.1">scikit-image</requirement>
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21 <requirement type="package" version="3.3.4">matplotlib</requirement>
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22 <requirement type="package" version="2020.10.1">tifffile</requirement>
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23 <requirement type="package" version="1.20.2">numpy</requirement>
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24 </requirements>
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25 <command detect_errors="aggressive">
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26 <![CDATA[
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27 python '$__tool_directory__/overlay_images.py'
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28 '$method_option.im1' '$method_option.im2'
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29 #if $method_option.method == "seg_contour"
22ff7c705a83 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8cd85b185acbfaa9ee6f4e9a389abc1f7b7c44bb
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30 ./output.png
22ff7c705a83 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8cd85b185acbfaa9ee6f4e9a389abc1f7b7c44bb
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31 #else
22ff7c705a83 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8cd85b185acbfaa9ee6f4e9a389abc1f7b7c44bb
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32 ./output.tif
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33 #end if
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34 --method $method_option.method
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35 #if $method_option.method == "blending"
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36 --alpha $method_option.alpha
bf590a9733ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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37 #elif $method_option.method == "seg_contour"
bf590a9733ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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38 --thickness $method_option.thickness
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39 --color '$method_option.color'
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40 $method_option.show_label
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41 --label_color '$method_option.label_color'
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42 #end if
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43 ]]>
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44 </command>
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45 <inputs>
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46 <conditional name="method_option">
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47 <param name="method" type="select" label="Type of the overlay">
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48 <option value="coloc_vis" selected="True">Colocalization</option>
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49 <option value="blending">Linear blending</option>
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50 <option value="seg_contour">Segmentation contours over image</option>
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51 </param>
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52 <when value="coloc_vis">
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53 <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" />
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54 <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" />
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55 </when>
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56 <when value="blending">
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57 <param name="im1" type="data" format="tiff,png" label="Image #1" />
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58 <param name="im2" type="data" format="tiff,png" label="Image #2" />
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59 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/>
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60 </when>
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61 <when value="seg_contour">
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62 <param name="im1" type="data" format="tiff,png" label="Intensity image" />
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63 <param name="im2" type="data" format="tiff,png" label="Label image" />
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64 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
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65 <param name="color" type="color" value="#ff0000" label="Contour color"/>
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66 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
2
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67 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
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68 </when>
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69 </conditional>
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70 </inputs>
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71 <outputs>
3
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72 <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff">
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73 <filter>method_option['method'] != 'seg_contour'</filter>
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74 </data>
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75 <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
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76 <filter>method_option['method'] == 'seg_contour'</filter>
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77 </data>
0
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78 </outputs>
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79 <tests>
3
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80 <test expect_num_outputs="1">
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81 <param name="im1" value="mask1.tif"/>
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82 <param name="im2" value="mask1r.tif"/>
1
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83 <param name="method" value="coloc_vis"/>
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84 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tif" ftype="tiff"/>
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85 </test>
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86 <test expect_num_outputs="1">
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87 <param name="im1" value="mask1.tif"/>
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88 <param name="im2" value="mask1r.tif"/>
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89 <param name="method" value="blending"/>
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90 <param name="alpha" value="0.3"/>
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91 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tif" ftype="tiff"/>
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92 </test>
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93 <test expect_num_outputs="1">
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94 <param name="im1" value="sample1_uint8.tif"/>
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95 <param name="im2" value="mask1.tif"/>
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96 <param name="method" value="seg_contour"/>
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97 <param name="thickness" value="2"/>
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98 <param name="color" value="#ff0000"/>
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99 <param name="show_label" value="--show_label"/>
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100 <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/>
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101 </test>
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102 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test -->
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103 <param name="im1" value="sample1_uint8.tif"/>
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104 <param name="im2" value="mask2.tif"/>
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105 <param name="method" value="seg_contour"/>
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106 <param name="thickness" value="2"/>
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107 <param name="color" value="#ff0000"/>
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108 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/>
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109 </test>
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110 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test -->
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111 <param name="im1" value="sample1_uint16.tif"/>
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112 <param name="im2" value="mask2.tif"/>
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113 <param name="method" value="seg_contour"/>
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114 <param name="thickness" value="2"/>
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115 <param name="color" value="#ff0000"/>
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116 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/>
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117 </test>
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118 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test -->
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119 <param name="im1" value="sample1_uint8_rgb.png"/>
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120 <param name="im2" value="mask2.tif"/>
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121 <param name="method" value="seg_contour"/>
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122 <param name="thickness" value="2"/>
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123 <param name="color" value="#ff0000"/>
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124 <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/>
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125 </test>
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126 </tests>
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127 <help><![CDATA[
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128
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129 **Overlays two images for visualization.**
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130
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131 This tool overlays two image to visualize *linear image blending*, *colocalization*, or *segmentation contours*
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132 over an intensity image. For *image blending* and *colocalization*, the input images must be single-channel 2-D
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133 images. For *segmentation contours*, the intensity must be a 2-D single-channel or 2-D RGB image.
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134
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135 ]]></help>
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136 <citations>
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137 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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138 </citations>
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139 </tool>